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- PDB-9in9: Structure of the viral channelrhodopsin OLPVR1 at low pH obtained... -

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Basic information

Entry
Database: PDB / ID: 9in9
TitleStructure of the viral channelrhodopsin OLPVR1 at low pH obtained by soaking
ComponentsViral rhodopsin OLPVR1
KeywordsMEMBRANE PROTEIN / rhodopsin / ChR2 / open state / open channel / ChRMine / cation-conducting ChR
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesOrganic Lake phycodnavirus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBukhdruker, S. / Zabelskii, D. / Astashkin, R. / Gordeliy, V.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE11-0029-02 France
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0026 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0015-01 France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2025
Title: Ion-conducting and gating molecular mechanisms of channelrhodopsin revealed by true-atomic-resolution structures of open and closed states.
Authors: Zabelskii, D. / Bukhdruker, S. / Bukhalovich, S. / Tsybrov, F. / Lamm, G.H.U. / Astashkin, R. / Doroginin, D. / Matveev, G. / Sudarev, V. / Kuzmin, A. / Zinovev, E. / Vlasova, A. / Ryzhykau, ...Authors: Zabelskii, D. / Bukhdruker, S. / Bukhalovich, S. / Tsybrov, F. / Lamm, G.H.U. / Astashkin, R. / Doroginin, D. / Matveev, G. / Sudarev, V. / Kuzmin, A. / Zinovev, E. / Vlasova, A. / Ryzhykau, Y. / Ilyinsky, N. / Gushchin, I. / Bourenkov, G. / Alekseev, A. / Round, A. / Wachtveitl, J. / Bamberg, E. / Gordeliy, V.
History
DepositionJul 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Viral rhodopsin OLPVR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81727
Polymers28,1271
Non-polymers7,69026
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint26 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.235, 115.755, 53.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Viral rhodopsin OLPVR1


Mass: 28127.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Organic Lake phycodnavirus (environmental samples)
Gene: 162281038 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: F2Y337

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Non-polymers , 5 types, 137 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-97N / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36O4
#4: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C20H42
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM Tris, 900 mM NaCl, and 24% (w/v) PEG 6000; Soaked: 100 mM sodium citrate pH 2.5, 900 mM NaCl, and 24% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.41→33.42 Å / Num. obs: 36461 / % possible obs: 92.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.97 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 13.1
Reflection shellResolution: 1.41→1.55 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1824 / CC1/2: 0.316 / Rpim(I) all: 0.952 / % possible all: 75.9

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Processing

Software
NameVersionClassification
MxCuBE3data collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AKY

7aky


Resolution: 1.41→33.42 Å / SU ML: 0.1651 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.9591
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218 1781 4.89 %
Rwork0.1877 34643 -
obs0.1892 36424 64.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.74 Å2
Refinement stepCycle: LAST / Resolution: 1.41→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 220 111 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822952
X-RAY DIFFRACTIONf_angle_d0.93123979
X-RAY DIFFRACTIONf_chiral_restr0.0745427
X-RAY DIFFRACTIONf_plane_restr0.006478
X-RAY DIFFRACTIONf_dihedral_angle_d15.71151097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.440.290650.3946165X-RAY DIFFRACTION4.06
1.44-1.490.3796250.3294391X-RAY DIFFRACTION9.78
1.49-1.530.3186480.2904851X-RAY DIFFRACTION20.99
1.53-1.590.3152660.31021258X-RAY DIFFRACTION30.93
1.59-1.650.34631040.31251868X-RAY DIFFRACTION45.88
1.65-1.730.3331160.29322527X-RAY DIFFRACTION61.48
1.73-1.820.31121470.27733291X-RAY DIFFRACTION80.61
1.82-1.930.27811860.24043794X-RAY DIFFRACTION91.49
1.93-2.080.24042070.19164070X-RAY DIFFRACTION98.89
2.08-2.290.19962040.17124083X-RAY DIFFRACTION98.42
2.29-2.620.20022340.16284048X-RAY DIFFRACTION97.94
2.62-3.30.19282020.16694120X-RAY DIFFRACTION97.32
3.3-33.420.21362370.18474177X-RAY DIFFRACTION95.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.536372574531-0.318507649023-0.1154151340730.6831078703560.334048605950.09691422585760.06248524603240.01274054795090.0570924694871-0.06362654423620.0148860843828-0.0120857562194-0.2969880230830.155524315150.0002194902259420.220853231135-0.0548852148503-0.004547533519510.2316080579890.0005149788289930.2438092920951.1577848985429.2224467102-1.30915513773
20.914522879862-0.4616239152180.2500621478730.673038142045-0.1353064630590.3031211059840.205036319864-0.006900561151370.07399725877630.08201712482470.0942417983042-0.10636749197-0.6276888285350.3109032498670.007874327866210.194414768443-0.0426485537214-0.01643719881120.17164471487-0.01901530386660.226634169172.932503633421.01966357121.60541148831
31.08836430501-0.3477471145790.013048281281.200700594740.02917597150831.17987615073-0.002048933764090.0535141874122-0.0958705501935-0.0377656196093-0.01330095860410.08032836662430.137324139721-0.0402677552439-0.0001959553268030.148687375791-0.000387000517556-0.01367222232620.135730567342-0.01366807418420.16696153901-8.6849737691110.6627132748-0.167743050647
40.960326061623-0.345969641773-0.03385196505490.853000909864-0.5095256682550.3170463193060.126288207809-0.0945334977893-0.01914709874150.005013551090520.118154438782-0.152885736675-0.1482016599970.1250710894240.0004980575965610.161951893052-0.00560601369458-0.01538585969960.166559975867-0.003217507750080.200301626202-5.7664546894124.9408548336-0.20015078963
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 31 )2 - 312 - 31
22chain 'A' and (resid 32 through 64 )32 - 6432 - 64
33chain 'A' and (resid 65 through 186 )65 - 18665 - 186
44chain 'A' and (resid 187 through 225 )187 - 225187 - 225

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